#!/usr/bin/perl

# Copyright 2013 O. Sotolongo <osotolongo@fundacioace.com>

use strict; use warnings;
use Parallel::ForkManager;
use GNTools qw(achtung);
use File::Basename qw(basename);
use constant CHROMOSOMES => 22;

my $max_processes = 4;
my $impute = '/usr/local/bin/plink --noweb --proxy-impute all --make-bed --allow-no-sex';
my $db = shift;
die "Must supply database\n" unless $db;
my $pm = new Parallel::ForkManager($max_processes);
my $logfile = "/tmp/.parallel_impute_by_db_output.log";
my $ordfile = "/tmp/.parallel_impute_by_db_orders.log";
open ORDOUT, ">$ordfile" or die "Can't open file, $!";
open STDOUT, ">$logfile" or die "Can't redirect stdout";
open STDERR, ">&STDOUT" or die "Can't dup stdout";
my $bndb = basename($db);

for(my $chr = 1; $chr <= CHROMOSOMES; $chr++){
        my $order = $impute.' --bfile '.$db.'_chr'.$chr.' --out '.$bndb.'_chr'.$chr.'_plink_imputed';
        $pm->start() and next;
        print ORDOUT "$order\n";
        system($order);
        $pm->finish;
}
$pm->wait_all_children;

close ORDOUT;
close STDERR;
close STDOUT;
achtung "plink impute", "La imputacion de plink ha terminado\n";
print "Have a nice day! ;-)\n";